
mkdir -p ${work_dir}/ARID1A

gene=ARID1A
${Rscript} ${scripts_path}/plot/Lollipop_variant.IGC_DGC.R \
--gene ${gene} \
--sample_public_info ${work_dir}/public_ref/combine/MutationInfo.combine.addMolecularSubType.tsv \
--cancer_file ${work_dir}/maf_public/All_use.addVAF.maf \
--cancer_nmu_file ${maf_path}/All_GGA.cancer.maf \
--sample_info ${work_dir}/baseTable/STAD_Info.addBurden.MSI_MSS.addCNVType.tsv \
--gtf_file ${ref_path}/GTF/gencode.v19.annotation.exonNum.gtf \
--out_path ${work_dir}/ARID1A


echo -e "Tumor\tchromosome\tstart\tREF\tALT\tt_ref_count\tt_alt_count\tgene\texon_pos\taachange" \
> ${work_dir}/ARID1A/ARID1A_28522256.tsv
cat ${work_dir}/ARID1A/28522256_ARID1A.tsv | grep -w ARID1A | awk -F'\t' '{OFS="\t"}{print $1,$2,$6,$10,$13,$18,$19}' | \
tr ',' '\t' | sed 's/"//g'  | tr '/' '\t' | tr ':' '\t' \
>> ${work_dir}/ARID1A/ARID1A_28522256.tsv